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Magnesium in PDB 4qzw: Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

Enzymatic activity of Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914

All present enzymatic activity of Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qzw was solved by E.M.Huber, W.Heinemeyer, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.660, 300.700, 145.380, 90.00, 113.22, 90.00
R / Rfree (%) 18.8 / 21.8

Other elements in 4qzw:

The structure of Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 (pdb code 4qzw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qzw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4qzw

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Magnesium binding site 1 out of 8 in the Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:45.9
occ:1.00
 O G:MET125 2.4 42.5 1.0
OG1 G:THR8 2.7 40.8 1.0
O G:ARG122 2.9 39.4 1.0
O G:TYR119 2.9 34.1 1.0
O G:ALA123 3.1 42.7 1.0
CG2 G:THR8 3.2 39.9 1.0
C G:MET125 3.4 42.1 1.0
CB G:THR8 3.5 40.2 1.0
C G:ALA123 3.7 43.3 1.0
CA G:ALA123 3.8 42.3 1.0
C G:ARG122 3.9 40.5 1.0
N G:THR8 4.1 43.9 1.0
C G:TYR119 4.1 32.7 1.0
CA G:ARG126 4.1 37.4 1.0
N G:ARG126 4.2 38.4 1.0
N G:MET125 4.3 44.9 1.0
N G:ALA123 4.4 41.3 1.0
CD G:PRO127 4.4 34.6 1.0
CA G:THR8 4.4 42.1 1.0
CA G:MET125 4.5 46.0 1.0
N G:TYR124 4.7 46.3 1.0
C G:ARG126 4.8 36.9 1.0
CA G:TYR119 4.8 31.0 1.0
N G:PRO127 4.9 34.8 1.0
C G:TYR124 5.0 44.4 1.0

Magnesium binding site 2 out of 8 in 4qzw

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Magnesium binding site 2 out of 8 in the Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:54.9
occ:1.00
 O I:SER180 2.6 38.8 1.0
O I:ASP177 2.7 42.2 1.0
O I:ALA174 2.9 45.1 1.0
OXT I:ASP204 3.5 68.1 1.0
C I:SER180 3.8 41.4 1.0
C I:ALA174 3.9 46.4 1.0
C I:ASP177 3.9 41.8 1.0
CA I:ASP175 4.1 47.7 1.0
O I:ALA178 4.4 45.5 1.0
NH1 Y:ARG19 4.4 59.9 1.0
N I:ASP175 4.4 46.4 1.0
C I:ASP175 4.4 47.7 1.0
C I:ASP204 4.5 66.3 1.0
O I:ASP175 4.5 49.3 1.0
CA I:GLY181 4.5 44.8 1.0
O I:ASP204 4.5 71.1 1.0
CA I:ALA178 4.6 41.8 1.0
N I:GLY181 4.6 42.4 1.0
C I:ALA178 4.6 42.9 1.0
NH2 Y:ARG19 4.7 58.7 1.0
N I:ASP177 4.7 40.8 1.0
N I:ALA178 4.7 40.6 1.0
OD1 I:ASP175 4.7 51.6 1.0
N I:SER180 4.7 40.3 1.0
CA I:SER180 4.8 41.8 1.0
CA I:ASP177 4.8 41.5 1.0
CZ Y:ARG19 4.9 57.0 1.0
CA I:ALA174 5.0 44.8 1.0

Magnesium binding site 3 out of 8 in 4qzw

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Magnesium binding site 3 out of 8 in the Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:55.8
occ:1.00
 O K:ASP168 2.2 39.8 1.0
O W:ASP204 2.3 58.8 1.0
O K:ALA165 2.4 42.7 1.0
O K:SER171 2.5 46.7 1.0
C K:ASP168 3.2 41.2 1.0
C W:ASP204 3.2 57.0 1.0
CA K:ALA169 3.6 44.0 1.0
C K:ALA165 3.6 42.8 1.0
CA W:ASP204 3.7 55.2 1.0
C K:SER171 3.7 44.0 1.0
C K:ALA169 3.7 45.7 1.0
O K:ALA169 3.8 45.7 1.0
N K:ALA169 3.8 43.2 1.0
NH1 K:ARG19 3.8 59.0 1.0
O K:HIS166 3.9 43.8 1.0
CB W:ASP204 3.9 55.1 1.0
N K:SER171 4.1 42.2 1.0
OXT W:ASP204 4.3 54.2 1.0
CA K:ALA165 4.3 42.8 1.0
C K:HIS166 4.4 44.2 1.0
CA K:ASP168 4.4 41.0 1.0
CA K:SER171 4.4 41.5 1.0
CZ K:ARG19 4.5 56.9 1.0
N K:TYR170 4.5 46.2 1.0
N K:ASP168 4.5 42.4 1.0
O W:HOH305 4.5 43.2 1.0
N K:HIS166 4.6 43.7 1.0
O K:ALA164 4.6 46.0 1.0
N K:GLY172 4.8 43.6 1.0
CA K:HIS166 4.8 44.2 1.0
C K:ARG167 4.8 44.7 1.0
NH2 K:ARG19 4.8 59.9 1.0
CB K:ALA169 4.9 43.4 1.0
CB K:SER171 4.9 39.2 1.0
CA K:GLY172 4.9 46.0 1.0

Magnesium binding site 4 out of 8 in 4qzw

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Magnesium binding site 4 out of 8 in the Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:40.0
occ:1.00
 O N:SER169 2.4 38.2 1.0
O N:ILE163 2.6 40.2 1.0
O N:ASP166 2.9 42.5 1.0
NH1 N:ARG19 3.5 42.4 1.0
C N:SER169 3.6 37.9 1.0
C N:ILE163 3.7 41.5 1.0
CD1 a:LEU34 3.7 44.2 1.0
C N:ASP166 3.9 41.6 1.0
CG2 N:ILE163 4.0 40.5 1.0
CZ N:ARG19 4.3 42.8 1.0
CA N:GLY167 4.3 40.9 1.0
CA N:GLY170 4.3 42.1 1.0
CA N:ILE163 4.4 41.2 1.0
O N:GLY167 4.4 36.4 1.0
N N:GLY170 4.4 39.9 1.0
NH2 N:ARG19 4.5 40.9 1.0
N N:GLY167 4.5 41.1 1.0
C N:GLY167 4.5 38.8 1.0
N N:SER169 4.6 36.9 1.0
CA N:SER169 4.7 35.8 1.0
N N:LYS164 4.7 43.7 1.0
CB N:ILE163 4.8 40.3 1.0
O N:LYS164 4.9 46.0 1.0
C N:LYS164 4.9 45.0 1.0
CA N:LYS164 5.0 44.7 1.0

Magnesium binding site 5 out of 8 in 4qzw

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Magnesium binding site 5 out of 8 in the Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg203

b:49.5
occ:1.00
 OD1 N:ASP51 2.5 30.8 1.0
OE1 H:GLN91 2.8 51.0 1.0
CG N:ASP51 3.4 28.8 1.0
CD H:GLN91 3.5 48.9 1.0
NE2 H:GLN91 3.5 50.3 1.0
OD2 N:ASP51 3.7 40.4 1.0
CE1 H:PHE88 4.0 31.0 1.0
O N:ASN92 4.2 56.6 1.0
CZ H:PHE88 4.4 30.8 1.0
CD1 H:PHE88 4.7 30.9 1.0
CB N:ASP51 4.8 30.5 1.0
ND1 H:HIS116 4.8 36.1 1.0
CG H:GLN91 4.9 44.5 1.0
OG N:SER48 5.0 44.0 1.0

Magnesium binding site 6 out of 8 in 4qzw

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Magnesium binding site 6 out of 8 in the Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:64.8
occ:1.00
 OXT L:ASP222 2.4 59.4 1.0
O V:ASP166 2.5 40.3 1.0
O V:ILE163 2.8 46.9 1.0
O V:TRP164 2.8 46.5 1.0
C L:ASP222 3.1 56.9 1.0
C V:ASP166 3.1 42.8 1.0
C V:TRP164 3.3 48.9 1.0
N V:ASP166 3.6 42.9 1.0
CA L:ASP222 3.7 55.2 1.0
N V:LEU167 3.7 42.6 1.0
O L:ASP222 3.8 57.0 1.0
C V:ILE163 3.8 49.0 1.0
O V:SER169 3.8 42.2 1.0
CA V:LEU167 3.9 43.7 1.0
C V:ASN165 3.9 44.4 1.0
N V:ASN165 3.9 48.2 1.0
CA V:TRP164 4.0 49.1 1.0
CA V:ASP166 4.0 42.5 1.0
CD2 V:LEU167 4.1 44.0 1.0
O L:ARG221 4.2 50.6 1.0
N V:TRP164 4.3 48.6 1.0
CD1 L:ILE35 4.3 45.9 1.0
CA V:ASN165 4.3 46.5 1.0
O V:GLY162 4.3 48.5 1.0
O V:ASN165 4.4 43.4 1.0
CB L:ASP222 4.7 55.3 1.0
N L:ASP222 4.8 53.9 1.0
C V:LEU167 4.9 41.8 1.0
NH1 L:ARG28 4.9 52.1 1.0
C L:ARG221 4.9 52.9 1.0
CG V:LEU167 4.9 44.4 1.0
CB V:LEU167 4.9 44.0 1.0
NH1 V:ARG19 5.0 55.1 1.0

Magnesium binding site 7 out of 8 in 4qzw

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Magnesium binding site 7 out of 8 in the Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:61.0
occ:1.00
 O Y:ASP168 2.2 38.8 1.0
O I:ASP204 2.3 71.1 1.0
O Y:ALA165 2.6 43.1 1.0
O Y:SER171 2.8 43.2 1.0
C Y:ASP168 3.2 41.4 1.0
C I:ASP204 3.2 66.3 1.0
CA Y:ALA169 3.4 44.4 1.0
N Y:ALA169 3.7 45.1 1.0
C Y:ALA169 3.7 42.8 1.0
CA I:ASP204 3.7 63.1 1.0
C Y:ALA165 3.7 41.9 1.0
O Y:ALA169 3.7 43.8 1.0
O Y:HIS166 3.8 45.0 1.0
NH1 Y:ARG19 3.9 59.9 1.0
C Y:SER171 4.0 40.9 1.0
CB I:ASP204 4.1 61.7 1.0
OXT I:ASP204 4.2 68.1 1.0
N Y:SER171 4.3 40.5 1.0
C Y:HIS166 4.3 43.0 1.0
CA Y:ASP168 4.4 41.0 1.0
N Y:ASP168 4.5 42.6 1.0
N Y:TYR170 4.5 40.6 1.0
CZ Y:ARG19 4.5 57.0 1.0
CA Y:ALA165 4.6 41.2 1.0
N Y:HIS166 4.7 43.4 1.0
CA Y:SER171 4.7 39.1 1.0
C Y:ARG167 4.7 43.9 1.0
O Y:ALA164 4.7 42.0 1.0
CB Y:ALA169 4.8 43.9 1.0
CA Y:HIS166 4.8 43.1 1.0
O Y:ARG167 4.8 46.9 1.0
NH2 Y:ARG19 4.9 58.7 1.0

Magnesium binding site 8 out of 8 in 4qzw

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Magnesium binding site 8 out of 8 in the Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ycp BETA5-C52F Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:59.3
occ:1.00
 O Z:THR192 2.7 52.6 1.0
O Z:VAL198 3.0 40.9 1.0
O Z:ASP222 3.2 63.9 1.0
O Z:HIS195 3.5 42.6 1.0
OD1 Z:ASP222 3.6 59.2 1.0
CG2 Z:THR192 3.6 53.4 1.0
C Z:THR192 3.8 52.0 1.0
NH2 Z:ARG28 4.0 53.6 1.0
NH2 H:ARG19 4.0 57.3 1.0
C Z:VAL198 4.2 45.6 1.0
C Z:ASP222 4.2 61.4 1.0
CA Z:THR192 4.3 51.5 1.0
O Z:ILE196 4.4 44.0 1.0
C Z:HIS195 4.5 42.2 1.0
CA Z:ILE196 4.5 42.1 1.0
CB Z:THR192 4.6 51.3 1.0
CG Z:ASP222 4.6 56.8 1.0
O Z:LYS220 4.7 61.8 1.0
C Z:ILE196 4.7 41.8 1.0
OXT Z:ASP222 4.8 59.3 1.0
CA Z:GLY199 4.8 49.0 1.0
CZ H:ARG19 4.8 51.6 1.0
CZ Z:ARG28 4.9 52.7 1.0
NH1 H:ARG19 4.9 51.4 1.0
N Z:GLU193 4.9 50.0 1.0
NH1 Z:ARG28 4.9 54.9 1.0
N Z:ILE196 5.0 41.8 1.0
N Z:GLY199 5.0 47.6 1.0

Reference:

E.M.Huber, W.Heinemeyer, M.Groll. Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and Onx 0914. Structure 2015.
ISSN: ISSN 0969-2126
PubMed: 25599643
DOI: 10.1016/J.STR.2014.11.019
Page generated: Tue Aug 20 02:42:24 2024

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